Table 3 – Interactive Molecular Visualization

 

 

Tactile Models

Virtual Models

Advantages

 

- shows connectivity

- displays the real 3D in ideal state

- possibility of illustrating some intramolecular interactions (internal rotation)

- can test superposition of isomers

- can generate possible conformer structures by internal rotation

- shows true arrangement plus distortions – based on real experimental measurements or computations such as Spartan

- can change orientation and mode of display (“true” size with space fill)

- can make measurements

    -bond length

    -bond angle

    -torsion angle

    -molecular dimensions

- can visualize complicated molecules (DNA, proteins) with simplifying modes of display

- provides flexibility – animated vibrations (stretch, bend, internal rotation of bonds)

- can generate animated reaction mechanisms

- can display electrostatic potential maps

    -molecular polarity

    -attack points in reactions

Disadvantages

- is rigid (set bond lengths and angles)

- true molecule size and shape not possible

- can fall apart! (at least some)

- may encounter incorrect structure files

- may not grasp the 3D nature on flat computer screen